After their first encounter, the Replicators created their own versions of Sheppard and McKay. They have their Memories, and are trying to understand them. The Replicators run with John and Rodney's Feelings for each other, engaging in a Sexual Relationship. The Relationship was always there, and through the eyes of the Replicators, with no restraints, and no boundaries, they're free to explore.

John Sheppard is getting married, to a woman that his team rescued from the Wraith several months earlier. He's asked McKay to be his best man, but Rodney is being torn apart, he hates this woman, but she hates him far more, so far doing her best to keep Rodney away from John. Rodney is in Love with John, and at his bachelor party, tells him. John is angry, uncharacteristically furious, but the next day, they have sex together before the ceremony, but can either let the wedding go ahead now?

A hot-headed Major has just arrived on Daedalus; he's got an attitude, and a problem with everyone, but most noticeably a problem with Sheppard. Getting into an argument with John in the Commissary; he calls John a "Faggot", and "Colonel Cocksucker". Everyone is stunned silent, but no one more than John himself, he's Straight; and doesn't know where that's come from. The Major is sent back to Earth, and no one on Atlantis who knows John is taking it seriously, but Officers that don't know him are being overly professional, and the relaxed air that John has always liked to adopt is gone. John is feeling very self conscious, people aren't engaging him, women aren't flirting with him, and he's even sure that he's caught people laughing at him. What he can't work out is whether or not this Guy hit a nerve with what he said, did he know something John doesn't? John has never been intimate with another Guy, has never wanted to be, but now he's having to put up with what it would be like if he actually was, and he doesn't like it. John starts getting defensive, even with his Friends, and goes so far as to blame Rodney, thinking that maybe their Friendship is being misconstrued.

John and Rodney are Ancients living in Atlantis that is still residing on Earth. John is head of their Military operations and Rodney is working with Janus in the Sciences. John and Rodney built/build the Puddle Jumpers together. Rodney also creates the personal shield that was in season 1x3 Hide and Seek. Any additional expedition members are optional. I think it would be cool to have it end where Atlantis leaves Earth, since that is how the series starts, but that too is also optional.

When two Englishmen arrive on Atlantis, they cause quite a stir; they were married in a Civil Partnership, and the Military might not like this, but Atlantis is a civilian run expedition. One of the men is a Royal Air Force pilot, the other a scientist, and their relationship is eerily familiar, the bickering, and affectionate sniping echoing that of another pilot, and another scientist. People begin to talk about the extent of Sheppard's relationship with McKay. John is easygoing, but it's getting uncomfortable, and there really isn't anything going on between them, and he and Rodney are forced to examine their relationship for themselves.

So I had a thought. What if the Pegasus Galaxy wasn’t as accepting of homosexuality as it is normally portrayed to be? What if homosexual relationships were seen simply unacceptable in a ‘world’ where populations were small and the birth of children was necessary for the survival of a culture? I’d love to see a fic. where John and Rodney are lovers and somehow they are put in a situation where their friendship with Ronon and Teyla is questioned or destroyed due to the latter’s belief that such a relationship is disgusting, selfish, and possibly even criminal. Maybe their own relationship is revealed or possibly they have to witness someone being punished for being gay; noting that both Ronon and Teyla agree that the individual(s) deserved to be reprimanded/penalized.

Sheppard's Ex Wife has been Posted to Atlantis, and John has never been more angry. She is stunning, but also vindictive, and seeing John's Friendship with Rodney, makes a play for him to annoy John. Rodney is loyal to John, but at the same time, when a beautiful woman comes on to him, which isn't all that often, he's not about to look a Gift Horse in the mouth. John is furious, and not quite sure who he's more furious with, but he soon realises that he's hurt, and that he's jealous.

What if there was an problem with the stargate? What if it brought a Dr John Sheppard from another universe? This Sheppard was working on a way to save his Atlantis from the wraith but a mixed up cause him to come to the "normal" universe. The thing is that he wanted a realtionship with Rodney in his universe but his Rodney died. Now Dr. Sheppard believes this is another chance to be with Rodney. But he is not the only Sheppard that wants Rodney. bottom Rodney please.
Extra points for kinky sex.
Extra points for sharing Rodney.
Extra Points for using the line. "It is a McKay sandwhich"

There is a lot of bdsm fics out there and reguardless of the pairing their dynamics usually turn out to be a perfect match. But what if they where not such a great match? If two doms attract/fall in love...or a dom and a switch etc. Then what happens? It might work for a while but eventually there will be needs that simply aren't met. What happens then?
That is the fic I'd like to read. When things aren't a perfect match. How do they solve that?
Slash story, bdsm.

John is in love with Rodney and everyone but Rodney knows, or at least suspects.
Everyone respects the pair of them enough to not tell Rodney since they, like John, believe that Rodney is straight. But then a new male arrival to the base takes an interest in the snarky scientist, an interest that Rodney seems to return.
Marines and Scientists alike do what they can to discourage Johnâ€™s competition but Rodney notices and jumps to the wrong conclusion, assuming that they disapprove on moral grounds, leaving him feeling hurt and disappointed.
John, meanwhile, is trying to play the supportive friend, but is secretly heartbroken.

Julia Donovan has been granted access to Atlantis, to continue her story for, if and when the existence of the Stargate is made public. She's exploring the city, interviewing personnel, and Sheppard has been assigned to show her around, and demonstrate the gene and its control of ancient technology. John takes her to the labs to meet McKay, and Julia is completely his type, but Rodney's interest isn't stopping her from coming onto John. She's asking them both about their personal lives, noticing the intimacy between them, asking some very awkward questions, and the journalist in her smelling a story, whether there's actually one to tell or not.

Looking through the Family Photos, John finds Pictures of his Father, his Grandfather, and even his Great-Grandfather, all with the same man. A beautiful man, looking to be in his mid 30's in all three series' of Pictures. John's Father is dead, he actually killed himself when he was a Baby; and John's Mother, like every woman in his Family, had abandoned him after he was born. John was raised by his Grandfather, his namesake, who's now in an Old Peoples' Home. John quizzes his Grandfather, who tells the story of the man; of Rodney, who had been Lover to every male descendant in their Family, and who he claims was an 'Ancient', whatever that is. He met John's Ancestor, and they fell in love, but Rodney didn't want to deny his Love the Family he craved, even after he was Married and a Father, their affair continued until the day he died, Rodney was that loyal. By this time, his Son was of age, and too fell in love with Rodney, this pattern continued, but John's Father couldn't live without Rodney and had killed himself. John wants to meet Rodney, angry about his Father, but also curious, and meeting him, Rodney isn't what John expected, and he falls in Love with him too, he doesn't want a Family, and Rodney mentions something called 'Ascension'.

In order to stay on Atlantis, John Sheppard started sleeping with one of the returning Ancients, and now a year later, and firmly established in a relationship with her, he's able to bring Rodney McKay back to Atlantis. John's changed, he's an honouree Ancient, talks like them, has even started to think like them, and hasn't had any contact with anyone on Earth in his time with them. Rodney, although glad to be back, has absolutely no respect for what John is doing, or for the act that he feels putting on, this isn't the John Sheppard he knew. A few walls begin to breakdown, and John starts to get angry at Rodney's disapproval, that anger spills over into something more, and before they know it, they start sleeping with each other, and after admitting that's the relationship that they both want, are now faced with not just a woman scorned, but an Ancient.

Slash or Gen. Wraith/Rodney or Wraith&Rodney friendship. (That Wraith must be male. It could be a OMC or Michael Kenmore or, if you really want, a Wraith!Sheppard.)

Prompt: Rodney McKay gets stuck on an uninhabited planet for 15 months, and his only company is a Wraith. There is no way for McKay and this Wraith to contact Atlantis or a Hive. Even though there was no other human on this planet, there are plenty local plant and wild life to support a human need for living. For survival, the Wraith needs to keep Rodney alive and healthy, and the astrophysicist rewards by letting the Wraith feed on him now and than. After some struggle on each side, they set in this life. They bonded with each other eventually.

(Someone finally finds them fifteen months later, but whether they go back, stay on that planet, or if they separate or stick together is up to the writer. What happen next, or what won’t happen next, is also up to the writer.)

The Ancients are still in control of Atlantis, and Sheppard and McKay have asked to return, surprisingly the Ancients are allowing this. It's not exactly the homecoming that they hoped, this is the Ancients' city, and there's not really anything for John and Rodney to do. The Ancients look on Rodney as though he was incompetent, Rodney's knowledge of Atlantis paling in comparison to theirs, and they're dismissive of him. One scientist is different, and Rodney feels an affinity for him. John is feeling even more put out than Rodney, the Ancients are more skilled in flying the Jumpers than he is, but like with Rodney, one Ancient is different, and he sets about teaching John how to fly like he does. Without realising it, both John and Rodney are getting involved with these Ancients, and the Ancients consider these full blown relationships. What John and Rodney don't know is if it's anything that they want, being with men. They only have each other to talk to about it, and ironically, they're the only men each other could ever have imagined being with.

Dr. Weir was killed shortly after arriving in Atlantis, and since it's a Civilian Expedition, McKay is left in charge. This is was out of Rodney's comfort zone, even though Sheppard is in a similar position, now Ranking Military Officer, and that they hardly know each other, Rodney still needs John's help in making this work for all of them.

Sheppard thinks that he's getting forgetful, asking for people in Departments who don't seem to be there, he assumes that it's just to do with crew rotations, and people coming and going on the Daedalus, but when he looks into things, he finds that there are no records of these people ever having been in Atlantis, people from his Life are disappearing, with those around him not remembering them at all. John is trying desperately to remind them, but the rewriting of their memories is eerily familiar, making John doubt himself. What starts with people on the edge of his perspective, moves on to those closest to him, and for each change, those that are left have their versions of history reconfigured to accept it, until one by one, only Sheppard and McKay are left, Rodney with no memory of it ever being any other way. Atlantis is deserted, with just John and Rodney left, and for Rodney, his relationship with John is the only relationship he has ever had, and for John, the only relationship that he has left.

McKay discovers one of the Ancient Communication Devices that Daniel Jackson used to reach the Ori Home Galaxy, but accidentally activates it himself, and his Consciousness is sent into someone there. Dr. Weir knows that if the Ori get a hold of Rodney, learn of Atlantis, or are able to track the signal, that they will begin an invasion of the Pegasus Galaxy as well. Sheppard is elected, well offers, well insists, on using the Device to get Rodney back, with his Gene; he might have more control over the process. Arriving in the Ori Home Galaxy, he finds Rodney, and their relief at finding each other leads to a surprisingly physical manifestation for both of them, as well as a Heresy to the Ori.

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